Climate Smart Agriculture Sourcebook

Genetic resources for Climate-Smart Agriculture Production

Production and Resources

Climate-smart management of aquatic genetic resources

Aquatic genetic resources are the genetic material (populations, individuals, gametes, DNA and alleles) of all aquatic plants and fish that provide food and related goods and services to humans, or that have potential to do so (Pullin and White, 2011). The world’s aquatic ecosystems contain over 150 000 species of fish, molluscs, crustaceans and aquatic plants (Bartley and Halwart, 2017). The world’s fisheries harvest over 2 000 species including fish, crustaceans, molluscs, coelenterates (e.g. jellyfish), echinoderms (e.g. sea urchins and sea cucumbers) and aquatic plants (FAO, 2014c). The number of farmed aquatic species is smaller, but still extremely high. FAO aquaculture production statistics have registered close to 600 species of fish and aquatic invertebrates and plants farmed around the world. However, only ten species (shellfish, crustaceans, plants and fin fish) account for half of the total aquaculture production (FAO, 2013a). Unlike terrestrial agriculture in which farmers have been using thousands of breeds and varieties for thousands of years, the domestication of aquatic species in aquaculture became more widely practiced only during the twentieth century (Nash, 2011). An exception is the common carp, which was domesticated centuries ago (Balon, 1995). Nonetheless, aquaculture is the fastest growing food production sector (8 percent average growth per year between 2006-2016) and is expected to play a major role in providing aquatic food in the future, as production from capture fisheries has plateaued (FAO, 2014c). As of 2014, about 50 percent of the aquatic food consumed comes from aquaculture (FAO, 2016c).

B8 - 6.1 Impact of climate change on aquatic genetic resources

Climate affects many aspects of aquatic environments, including water temperature; oxygenation; the acidity, salinity and turbidity of seas, lakes and rivers; the depth and flow of inland waters; the circulation of ocean currents; and the prevalence of aquatic diseases, parasites and toxic algal blooms. The impacts of climate change on fisheries and aquaculture are addressed in detail in chapter B4 -3.1. This chapter addresses the specific impacts of climate change on aquatic genetic resources.

Acidification of seawater, caused by increasing levels of carbon dioxide in the atmosphere (Nellemann, Hain and Alder, 2008) may compromise the role calcifying organisms play in sequestrating carbon, especially in shore areas. This will slow the growth rate of many aquatic species of molluscs and certain crustaceans, including zooplankton, and will have implications for the whole structure and functions of aquatic ecosystems. Over the long term, climate change is also expected to change some ocean currents, affecting the migration routes of some aquatic species and the dispersal of eggs and larvae (FAO, 2015b).

Rising temperatures affect the distribution and abundance of marine organisms. Some warm-water aquatic species are shifting towards the poles, and driving some native cold-water species towards extinction. In most environments, higher temperatures promote an increase in the productivity and growth rates of aquatic organisms. However, higher temperatures may also disrupt the timing of reproduction, negatively affect life cycles, limit the availability of food supplies or increase the prevalence of diseases, parasites and predators. Many aquatic organisms depend on having stable biological communities around them (FAO, 2015b). They are therefore vulnerable not only to direct effects on their own physiology, but also to disruptions that may occur because of the impacts climate change has on other organisms (Guinotte and Fabry, 2008). Some aquatic communities are reliant on particular species, such as corals, kelp, mangroves and sea grass. If these species are unable to adapt, whole communities will be disrupted and may disappear completely. Extreme weather events may lead to escapes from fish farms, with adverse effects on the genetic diversity of wild populations (FAO, 2015b).

Estuaries, lagoons and other coastal brackish waters are likely to be affected in several ways by climate change (Bates et al., 2008; Andrews, 1973; Smock et al., 1994). These environments are particularly vulnerable to hurricanes and storms, which are predicted to become more frequent under climate change. Rising sea levels will also be a threat. Heavy rainfall over the land may increase the runoff of freshwater, nutrients, sediments and pollutants into coastal waters (FAO, 2015b).

Many rivers will be affected by changing patterns in precipitation and evaporation (Ficke, 2007; MEA, 2005). More frequent droughts increase the risk that small lakes and rivers will dry out completely, creating barriers to waterbody connectivity and fish migration, major disruptions of local fisheries and threats to biodiversity. Unusually heavy rains may result in extreme flooding, temporarily merging previously separated water bodies and facilitating the introduction and spread of invasive species (FAO, 2015b). Runoff increases turbidity and siltation, which can lead to the elimination of aquatic species that require very clear water (e.g. giant clams and corals feeding through symbiotic zooxanthellaexxi). Turbidity also lowers light penetration and reduces the abundance and activity of the phytoplankton that form the basis of most aquatic food webs. For other species, it also hampers vision making it harder to feed, reproduce and avoid predators. Siltation can lead to the physical burial of sessile organisms, such as corals and bivalves (FAO, 2015b). Greater availability of nutrients can also cause rapid increases in the abundance of some invertebrates (Flint, 1985). Runoff can also generate harmful algal blooms or pollute the water (De Casablanca et al., 1997). Harmful algal blooms are also likely to increase as waters become warmer, threating coastal aquaculture and fisheries. Climate change may also favour some microbial pathogens and promote the spread of diseases among aquatic populations. Where the direct effects of climate change are combined with increasing water abstraction and other anthropogenic pressures, the loss of significant numbers of aquatic species may occur. 

Climate change will increase physiological stress in some farmed aquatic species populations, affecting productivity and susceptibility to certain diseases. However, in some areas, higher temperatures may also increase the ranges of some fisheries and allow the farming of some aquatic species in new areas and with increases in growth rates and productivity (FAO, 2015b).

B8 - 6.2 Characterization, evaluation, inventory and monitoring of aquatic genetic resources

More than 150 000 species of finfish, molluscs, crustaceans and aquatic plants have been described and recorded in various databases. FAO production statistics show that almost 600 species are being used in aquaculture (Bartley and Halwart, 2017). Information is largely at the species level (FAO, 2017b). Despite a much shorter history of domestication and genetic improvement compared to agriculture, the processes of domestication and selection have created significant inter- and intra-specific diversity, in the form of specific strainsxxii, varietiesxxiii, stocksxxiv, hybridsxxv, polyploidsxxvi and other genetic types (see also module B4 on climate-smart fisheries and aquaculture). Many identification tools are readily available (FAO, 2013b) and are becoming increasingly refined with the advance of molecular technologies. 

Genetic information and technologies, which are useful for coping with and mitigating climate change, are not commonly used in fisheries and aquaculture. In aquaculture, the switching from one species to another has been a successful strategy for coping with disease outbreaks or other problems. This may also be an option for the sector for responding to the impacts related to climate change. Although genetic information has been used for the development and management of some aquatic species, examples are usually limited to a few commercially important species in developed countries.

B8 - 6.3 Sustainable use and development of aquatic genetic resources for climate change adaptation

Climate change will have impacts on availability of freshwater resources and ambient temperatures, which will have consequences for the survival, spawning and migration of aquatic species. Different species will have varying abilities to tolerate changes to the changing environmental conditions. Indirect impacts on aquatic organisms will result from changes in ecosystem functions. The impacts of climate change are expected to be greater in equatorial and tropical regions, where aquatic species live at the upper end of their thermal tolerance.

From the perspective of genetic resources development, there is little that can be done to promote adaptation to climate change among the target species of wild capture fisheries production systems. As discussed in module B4 on climate-smart fisheries, adaptation actions are linked mainly to environmental management, which typically involve the maintenance of water quality, flow and connectivity, and the protection of habitat. In some instances, it is possible to restock aquatic ecosystems with wild or hatchery-reared fish that have the appropriate environmental adaptations. This can be used to restore production in irreversibly damaged systems. However, restocking can also have large and irreversible genetic effects on surviving wild populations. When maladapted farmed species are introduced into open waters, they can breed with wild relatives and threaten their viability or simply displace them. One typical maladaptation in farmed fish is the trait of precocious breeding or out-of-season breeding. This is due to on-farm selection for early spawning or later migration, which is preferred in aquaculture systems. However, this trait causes fish to respond inappropriately to environmental cues for breeding and migration. 

Aquaculture as a managed food production system has greater potential for adaptation to climate change than capture fisheries. It is potentially a climate-smart production system, particularly for the opportunities it offers for raising low trophic level species that have a lower carbon footprint than many intensive livestock systems. 

There is a considerable diversity of aquaculture species across a wide range of taxa (Table B8.3) with the greatest diversity in the Asia. More species are used in marine and coastal aquaculture (526) than in inland aquaculture (441).

Table B8.3. Diversity of aquaculture species by region.

All aquaculture
























Other animals












Total - all aquaculture taxa












Total by environment

Marine and coastal







Inland aquaculture







This genetic diversity in aquaculture food production shows the tremendous potential that exists to use genetic information and technologies for reducing risk, responding to external shocks and climate change, and accommodating changes in consumer demands or government policies (Singh, Boukerrou and Miller, 2010; Harvey et al., 2017). Some of these species can be used not only to produce food but other products, such as pharmaceuticals and biofuels. Aquaculture is a new and rapidly diversifying production sector, so there have been relatively little improvements made in the genetic resources that are used. However, where efforts have been made to systematically improve the breeds used in aquaculture, the results indicate that selective breeding can increase aquatic food production by 5 to 12 percent per year (Gjedrem, Robinson and Rye, 2012). There are financial and management challenges to overcome for improving genetic resources used in aquaculture, which is why significant progress has been made with only a handful of species so far. The focus has largely been on typical domestication objectives, such as increasing production, improving feed conversion, accelerating growth rates and strengthening disease resistance.

B8 - 6.4 Sustainable use and development of aquatic genetic resources for climate change mitigation

With over 70 percent of the planet covered by water, marine and freshwater ecosystems and their biota account for the largest carbon and nitrogen fluxes on the planet and also serve as its largest carbon sinks (Pullin and White, 2011). Terrestrial aquatic ecosystems include wetlands, rice fields, peatlands, mangroves, rivers, streams, ponds and lakes. In marine ecosystems, there are many coastal and oceanic processes that cycle and sequester nitrogen and carbon. Aquatic ecosystems and their associated biodiversity have immense importance and offer future potential for mitigating climate change.

As is the case with all agricultural sectors, food production from aquaculture and fisheries depends on ecosystem goods and services. The extent to which ecosystem habitats and processes deliver these goods and services is linked to the integrity of the ecosystem. Aquatic genetic diversity is an important component of ecosystem integrity. Environmental changes, both anthropogenic and climate driven, can disturb the integrity of the ecosystem and disrupt it functions, including those that contribute to climate change mitigation. For example, the sequestration of carbon in coral is affected by bleaching, which in turn is linked to sea temperature and nutrients. Likewise, wetlands and peatlands (see Box B7.2) can sequester carbon and organic matter, but will only do so when maintained in permanently wet conditions. Disturbances on peatlands, especially drainage, result in rapid mineralization of stored carbon – a process that releases carbon dioxide emissions. Managed wetland landscapes, such as rice farming systems (see chapter B1 - 3.1), also release greenhouse gases, primarily methane. 

Food production is one of the principle human activities that drive change in aquatic ecosystems. Other drivers of change include pollution and water use for other economic sectors. Efforts need to be made to minimize the impacts of these diverse forces on aquatic ecosystem functions. There are a range of cross-sectoral interventions that can serve to mitigate these impacts. In the terrestrial domain, most of these interventions revolve around the reduction of the impacts of climate change on hydrological regimes. This is done through better watershed management, particularly erosion and pollution control, which can be partly accomplished through the sustainable soil and land management practices, which are dealt with in module B7. The maintenance of freshwater connectivity is critical as it allows aquatic species to migrate and breed. Conserving and restoring damaged and threatened coastal areas, for example, by replanting mangroves, is also important. Other cross-sectoral forms of land and water management linked to food production that could contribute significantly to climate change mitigation include the integrated crop-aquaculture production systems (e.g. fish raised in flooded rice fields) and multitrophic mariculture. Potential approaches that need further research and trial development include the redesign of reservoirs and management of natural lakes to minimize their greenhouse gas emissions. 

There is a need to appraise the practical application of aquaculture and fisheries systems that extract and capture nutrients, particularly carbon, and the mass production and harvesting of micro-and/or macroalgae as feedstocks for clean biofuels.

B8 - 6.5 Conservation of aquatic genetic resources

In situ and ex situ conservation are both important for the conservation of aquatic genetic diversity, the development of commercial applications for this diversity, and its application to support climate change adaptation and make improvements in aquaculture species and breeds.

Intraspecific genetic characterization in terms of local populations, stocks and strains of aquatic genetic resources is an essential first step in the conservation of these resources (see chapter B8 - 6.2). Within a given species, distinct populations can tolerate different ranges of ecological conditions and they will have different levels of susceptibility to climate change. This aspect deserves particular attention in the in situ conservation of fish stocks in fisheries management. The traditional definition of a fish stock is usually geographically based and does not always consider that a given stock can be made up of distinct locally adapted populations requiring different management approaches (Bonanomi et al., 2015). Aquatic species tend to track closely their temperature boundaries of tolerance over generations, shifting their geographical range as the water warms. On a global scale, climate change is contributing to redefining aquatic species spatial distributions and the composition of biological communities at an increasing rate. To best adjust to these shifts in the ranges of species and populations, a traditional in situ conservation approach that mainly relies upon the retention of historical conditions in designated protected areas in marine, brackish and freshwaters may no longer be applicable in many cases. For this reason, there is a need for a critical reconsideration of conservation laws and programmes (Pecl et al., 2017).

Combined with in situ management, the ex situ conservation of aquatic genetic resources of farmed species and their wild relatives in aquaculture facilities, culture collections, gene banks, research facilities, zoos and aquaria is essential to preserve the different stages of an organism's life cycle. For example, the cryopreservation of sperm, embryos and tissue DNA allows for the maintenance of genetic diversity that may be useful or potentially useful for coping with the impacts of climate change.

According to preliminary data submitted by countries for the State of the World on Aquatic Genetic Resources for Food and Agriculture (FAO, 2016d), 600 species are actively conserved in situ through protected and managed areas. Some countries consider that protected areas are effective for conserving aquatic genetic resources. Seventy percent of surveyed countries have current ex situ conservation programmes. The genetic resources of more than 344 aquatic species are the subject of ex situ conservation programmes in 112 facilities in 47 surveyed countries. The potential of these species for climate change adaptation is seen as the lowest priority for ex situ conservation programmes. It is important to raise awareness about the value of adaptation and the need to establish ex situ aquaculture facilities to maintain fish germplasm of threatened species used in aquaculture operation and restocking programmes. Aquatic plants and micro-algae collections are easier to maintain. Many species and strains of aquatic microalgae are kept as ex situ tissue culture collections.  

Living on-farm gene banks of some species do exist, which would qualify as in situ on-farm conservation. However on-farm in situ conservation and on-farm ex situ conservation are often difficult to distinguish. For on-farm in situ conservation, the farm would need to maintain the desired species in a stable production environment, with no further genetic alteration or manipulation to occur. Most of these conditions do not exist in commercial farming operations because adaptive management to maintain profitability is the first priority. As a result, the desired species would adapt to the production environment over time, and this could not be considered the genetic conservation of the original strain (Lorenzen et al., 2013).